tbuckley/cabot-search huggingface dataset:
OS03.7.A AUTOFLUORESCENCE BASED RECOGNITION OF BRAIN TUMORS WITH A CONVOLUTIONAL NEURAL NETWORK
Authors: S Richter, J Dremel, T Wang, I Eyüpoglu, J Czarske, K Kirsche, R Kuschmierz, W Polanski, O Uckermann
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND The delineation of malignant brain tumors from surrounding tissue is crucial for maximal safe resection. Existing tools for intraoperative tumor visualization lack the possibility of real-time tissue classification. We therefore built a coherent fiber bundle (CFB) endoscope for autofluorescence imaging and trained a convolutional neural network (CNN) to distinguish tumor tissue (T) and non-tumor tissue (nT) in an ex vivo proof of concept study. MATERIAL AND METHODS The T-cohort included frozen tissue sections of 35 glioblastoma and 30 brain metastasis patients (10 breast cancer, 10 melanoma, 10 lung cancer). The nT-cohort comprised frozen tissue sections of hippocampi and temporal lobes from 23 patients undergoing surgery for epilepsy treatment. For image acquisition, a laser with excitation wavelength of 473 nm was coupled into a CFB and tissue autofluorescence between 500-550 nm was collected using a bandpass filter. The acquisition time of the camera was set to 700 ms. A CNN (VGG-19) was trained to differentiate the labels T from nT wherein the ground truth was defined by histopathological diagnosis. Training, validation and test sets were randomly generated across all patients in 66.6% / 16.6% / 16.6% proportion. Set generation was repeated 5 times and reported results for the independent test sets are mean values of all iterations. RESULTS In total, 3259 CFB images were acquired (T:2408, nT:851), with usually 40 CFB images per sample. Removal of CFB background was not improving classification accuracy and thus, was not performed. The classification accuracy of the CNN with a threshold probability of 0.5 for T-label assignment was 0.986 (sensitivity: 0.988, specificity: 0.982) for analysis of images and 0.98 (sensitivity: 0.971, specificity: 1) when calculating the result for each patient. To simulate clinical application where correct identification of healthy tissue is essential, we created a specificity-tuned CNN with adjusted threshold probability of 0.9 for T-label assignment. This led to a decreased accuracy of 0.945 but increased specificity on the image evaluation approach to 1 (sensitivity: 0.92). CONCLUSION Autofluorescence imaging through a CFB is capable of ex vivo recognition of brain tumor tissue with a CNN. The simplicity of the setup and minimal need for data pre-processing allows for intraoperative implementation and potentially enables real-time in vivo brain tumor delineation. To realize intraoperative transition, analysis of ex vivo bulk tissue will be upcoming to capture the signal complexity caused by tissue depth.
P06.03.A IMMORTALIZED MACROPHAGES AS A TOOL TO STUDY PHAGOCYTOSIS AND POLARIZATION <i>IN VITRO</i>
Authors: R RoyChoudhury, J A Hossain, R Bjerkvig, H Miletic
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Macrophages, an important element of the tumour-microenvironment (TME), are classified based on polarization state: tumour inhibiting ‘classically-activated macrophages’ M1 and tumour promoting ‘alternatively-activated macrophages’ M2. It is wellknown that the glioblastoma (GBM) TME is dominated by immunosuppressive M2 macrophages contributing to tumor growth by promoting angiogenesis, invasion and immunosuppression. However, macrophage culture is difficult to maintain as the cells do not proliferate and expand, making co-culture studies challenging. In this work, we successfully immortalized and expanded bone marrow derived mouse macrophages (BMDMs) that can be used as a tool to study phagocytosis and polarization in co-culture with tumor cells. MATERIAL AND METHODS Primary macrophages, obtained from the bone marrow of C57/BL6 mice, were transduced with two lentiviral vectors: hTERT with antibiotic hygromycin (Hy) and Simian virus 40 (SV40) with mCherry selective markers. Viral-titers were prepared by co-transfecting HEK293T with hTERT and SV40 constructs and plasmids MDL-X (Gag/Pol):Vpx. Vpx is a virion-packaged accessory protein that induces degradation of SAMHD1, a GTP- activated dNTP hydrolase that inhibits lentiviral infection of macrophages. BMDMs transduced with hTERT were subjected to gradient Hy selection after 5 days infection and SV40.mCherry positive cells were sorted by flow cytometry. To assess phagocytotic capacity, BMDMs were incubated with apoptotic bodies of a murine GBM cell-line (GL261) which was treated with HSV-TK/ganciclovir (GCV) suicide gene therapy. Phagocytosis was measured by fluorescence microscopy and flow cytometry. Further, BMDMs were externally induced with either E. coli lipopolysaccharide (LPS) and interferon gamma (IFNγ) or interleukin 4 (IL4) to activate M1 and M2 polarization. Flow cytometry was used to detect iNOS, CD40 and CD86 markers for M1 phenotype and Arginase1 and CD206 for M2. RESULTS hTERT.MDL-X.Vpx.Hy BMDM showed no clear signs of immortalization with limited proliferation followed by cell death. In contrast, SV40.MDL-X.Vpx.mCherry BMDM exhibited proliferative expansion from single colony, efficient freeze-thaw cycles and were used for further studies. BMDMs showed successful phagocytosis of apoptotic bodies from HSV-tk/GCV treated GL261 cells with an increasing capacity upto 18 hours of application. The phagocytic capacity was higher compared to commercial cell lines such as BV2 and Raw 264.7. Immortalized BMDMs tend to have a M2 phenotype without external induction and it is possible to activate M1 phenotype by LPS and IFNγ induction. CONCLUSION Here, we successfully immortalized bone-marrow derived macrophages and showed that they can be used as a tool to study macrophage polarization and phagocytic capability in a tumor immunotherapy context.
P01.08.B MENTAL FATIGUE IN PATIENTS WITH LOW-GRADE GLIOMA: ASSOCIATIONS WITH NEUROCOGNITIVE FUNCTIONING AND TUMOR CHARACTERISTICS
Authors: A M Buunk, F F Siebenga, M C A Kramer, F Gelens, F Gelmers, S E Rakers, I Bosma, R H Enting, A van der Hoorn, H L van der Weide, J M Spikman
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Fatigue is a frequent consequence of low-grade glioma (LGG), but the causes are still barely understood. Specifically mental fatigue might be related to cognitive impairment such as mental slowness and decreased attention. Also, patients with greater tumor volumes or tumors in certain locations (such as the frontal cortex) might have more cognitive impairments and experience more fatigue. The aim of the present study was twofold: (1) to examine the relationship between mental fatigue and information processing speed and complex attention and (2) to investigate the associations between mental fatigue and tumor volume and location in patients with LGG. MATERIAL AND METHODS 124 patients with LGG (IDH mutated astrocytoma and oligodendroglioma grade 2 and 3) were included before the start of proton therapy. Different facets of fatigue, including mental fatigue, were measured after surgery, with a multidimensional fatigue scale, the Dutch Multifactor Fatigue Scale (DMFS). The Vienna Test System was used to examine simple information processing speed, response inhibition, and divided attention. Tumor location and tumor volume (radiation target volume) were scored on the pre-radiotherapy MRI scan. Descriptive statistics, Spearman’s correlations, and between group comparisons were performed. RESULTS 41% of patients with LGG reported severe mental fatigue. No significant differences were found in mean performance on simple information processing speed, response inhibition and divided attention between severely mental fatigued patients and non-severely mental fatigued patients. However, the percentage of patients with impaired divided attention was significantly higher in the severely mental fatigued group (39%) compared to the non-severely mental fatigued group (16.2%), χ2 = 7.6, p &amp;lt; 0.05. No significant relationships were found between mental fatigue and tumor volume and location. Also, tumor location was not related to neurocognitive functioning, but larger tumor volume was significantly associated with poorer performance on divided attention (r = -0.19, p &amp;lt; 0.05). CONCLUSION A high rate of mental fatigue was found in patients with LGG. Furthermore, a relationship between impaired divided attention and severe mental fatigue was found. This implies that patients may develop mental fatigue due to increased cognitive efforts to compensate for attentional deficits. This might be especially important in patients with larger tumors, considering the relationship between tumor volume and divided attention. The results stress the importance of neuropsychological assessment in this patient group before the start of adjuvant treatment, to timely offer individual rehabilitation.
P16.03.A DEVELOPMENT OF INTRATHECAL DRUG DELIVERY PLATFORM TO CURE BREAST CANCER LEPTOMENINGEAL DISEASE BY DENDRITIC CELL VACCINE IN PRECLINICAL MODEL
Authors: V Law, C Snyder, L Macaisa, S Garg, B Czerniecki, P A Forsyth
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Leptomeningeal disease (LMD) is a rare form of metastasis in the meninges, a membrane surrounding the brain and spinal cord. Approximately 5% of advanced stage breast cancer (BC) will develop LMD and currently there is no cure. One reason for poor prognosis is the issue of drug accessibility to tumor sites due to the blood brain barrier (BBB) and blood-cerebral spinal fluid (CSF)-barrier. While the Ommaya reservoir is used clinically to overcome this challenge, there has not been an optimized preclinical model that allows researchers to adequately test novel therapies in the CSF space. MATERIAL AND METHODS The Forsyth lab have recently developed an MRI-compatible device called the “murine Ommaya” which mimics the Ommaya reservoir and allows repeated intrathecal (IT) administration of drugs in 3-7μl volume directly into CSF, bypassing BBB. In a joint effort with Dr. Czerniecki, whose lab have developed a pipeline for screening immunogenic MHC class II peptides from tumor-associated oncodrivers and subsequently generating tumor-targeting dendritic cells (DC), we have created a platform to IT deliver peptide-pulsed DCs directly targeting BC-LMD. RESULTS Currently, we have tested the efficacy of treatment in HER2+ LMD and triple negative breast cancer (TNBC) LMD models and found a very favorable response; LMD mice that received IT DC therapy exhibited reduced tumor burden and prolonged survival, and is more superior than systemic therapy. About 70% of mice from HER2+ LMD and 30% from TNBC LMD were cured of disease. Cured mice also exhibited resistance against LMD recurrence. CONCLUSION Our preliminary data suggest IT DC immunotherapy is effective against the incurable BC-LMD. We are currently investigating the mechanism(s) by which IT DC-initiated CD4 Th1 adaptive immune response against LMD. By using single-cell RNA-sequencing technique, we are analyzing the immune landscape in CSF tumor microenvironment in response to IT DC. FDA-approved phase I clinical trial has been funded by the US Department Of Defense. Future approach includes employing our IT DC vaccine platform in other cancer types, such as LMD from melanoma.
P10.19.A COMBINED TREATMENT USING MAPK AND PI3K SIGNALING PATHWAYS INHIBITORS EFFECTIVELY REDUCES GROWTH OF MELANOMA BRAIN METASTASIS CELLS <i>IN VITRO</i>
Authors: M Sættem, J Wang, T Sundstrøm, F Thorsen
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Brain metastasis is associated with poor prognosis, and median survival time from the time of diagnosis for cancer patients with brain metastases is only a few months. Brain metastases are estimated to occur in 20-40% of cancer patients. All solid tumors may spread to the brain, but the risk of developing brain metastases is higher in breast cancer, lung cancer and melanoma. Standard treatment of melanoma brain metastases (MBM) includes radiation therapy and surgery. In melanoma, the mitogen activated protein kinase (MAPK) and the phosphoinositide 3-kinase (PI3K) signaling pathways are often activated by genetic alterations. An activation mutation (BRAFV600E) in the MAPK pathway is commonly found in melanoma refractory to therapy. This mutation leads to increased proliferation and tumor cell survival. Previous studies show that BRAF-inhibitors block the increase in cell proliferation induced by the activated BRAF gene, however, many of the patients develop drug resistance within a few months. Objectives: In this project, we aimed to show that drugs targeting BRAF (vemurafenib) and PI3K pathways (buparlisib) used in combination effectively inhibit growth of treatment resistant MBM cells. MATERIAL AND METHODS Our research lab has previously developed human MBM cell lines, which have been made resistant towards vemurafenib treatment. To study the potential antitumoral effects of combined treatment we used these cells in several in vitro assays such as cell viability and proliferation, cell migration, colony forming assay, spheroid growth, apoptosis by IncuCyte and western blot to confirm effects on signaling pathways. RESULTS We found that combination treatment reduced the viability of resistant MBM cells, as well as their ability to proliferate. Further, the cells showed less ability to migrate after therapy. Altered cell morphology was also seen. Initial results show effects on colony formation and increased apoptosis after combined treatment. CONCLUSION A combination of MAPK and PI3K inhibitors effectively inhibits growth and viability of treatment resistant human MBM cells, compared to single drug treatment alone. The results support clinical use of combined therapy for melanoma patients with metastatic disease.
P11.34.A MULTIFACTORIAL ANALYSIS OF SURGICAL TREATMENT OF INTRACRANIAL METASTASES IN ELDERLY PATIENTS
Authors: A Gubian, A Sulejmani, A M Ruder, F Giordano, G Rinkel, N Etminan, S Brehmer
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Due to increasing age of the population, the number of elderly patients with brain metastasis accessible for surgery is increasing. The higher risk of peri-procedural complications and a reduced ability to tolerate aggressive treatment are often thought to limit intracranial surgery in older patients. However, little data are available on results of surgical brain metastasis treatment in elderly. In a subset of older patients who underwent surgical removal of brain metastases, we assessed the influence of age on survival and postoperative dependency. MATERIAL AND METHODS This is a retrospective observational study of patients over 65 years of age who underwent surgery for intracranial metastases between 2015 and 2022 at the Department of Neurosurgery, University Hospital Mannheim (Germany). The population was divided into group A (65-74 years old) and group B (75 years or older). The Eastern Cooperative Oncology Group (ECOG) score was used to assess functional status and independence. The primary endpoints were overall survival and the likelihood of remaining independent (ECOG &amp;lt;3) at 6 weeks. A wide range of clinical and radiological baseline factors were analysed. RESULTS 80 patients were included in the analysis. The mean age in the overall cohort was 73.2 years, and 74% of patients had a preoperative ECOG score of 2 or less. 48 patients were included in group A and 32 in group B. The 1-, 2- and 3-year probabilities of overall survival were 31%, 23% and 16% in group A and 38%, 23% and 23% in group B (p-value=0.61). Functional status in the overall cohort remained stable after surgery for most patients (70%), while 17% experienced a decline and 13% an improvement. 42 (88%) and 43 (90%) patients in group A were independent before and after surgery, respectively. 27 (84%) and 26 (81%) patients in group B were independent before and after surgery, respectively. 33 (69%) patients in group A and 19 (59%) patients in group B were independent at follow-up (p=0.65). No significant difference was found between the two groups for independence status preoperatively, postoperatively as well as at follow-up (p-values 0.69, 0.29 and 0.32, respectively). CONCLUSION In our analysis, neither survival nor outcome after surgery for brain metastases showed a correlation with age. Age alone should not be a barrier to intracranial surgery in carefully selected elderly patients with intracranial metastases.
P03.10.A IDENTIFYING DNA DAMAGE RESPONSE (DDR) RELATED FACTORS ESSENTIAL FOR RADIOTHERAPY RESPONSE IN GLIOBLASTOMA USING A NOVEL CRISPR/CAS9 LIBRARY, DDRKOL
Authors: I Kok, C Bayraktar, A Durgun, A C Aksu, A Kayabolen, O Yedier Bayram, I Sur Erdem, T Bagci Onder
Journal: Neuro-Oncology (2023)

Abstract The standard treatment of glioblastoma, which is the most common and aggressive primary brain tumor, includes combined radiotherapy (IR) and chemotherapy (temozolomide (TMZ)) after surgery. The basic working principle behind radiotherapy is to induce DNA double-strand breaks (DSBs), which is the most lethal form of DNA damage and the primary cause of cell death, and to finally kill cancer cells. Additionally, exposure to IR induces the activation of a multicomponent signal transduction network of DNA damage response (DDR). In this study, we developed a new CRISPR/Cas9-based tool to investigate the role of DDR mechanisms and identify novel genes affecting radiotherapy response in glioblastoma. We generated a focused sgRNA library termed DDRKOL (DNA Damage Response Knock Out Library) targeting the DDR pathway to identify novel modulators of TMZ and radiotherapy response with CRISPR/Cas9 screening in vitro. DDRKOL includes a total of 9000 sgRNAs targeting 888 genes (10 sgRNA/gene) containing all DNA damage-related pathways, curated from Gene Ontology Consortium, 35 sgRNA positive controls targeting cell essential genes, 90 non-targeting control sgRNAs, and 35 internal control genes. The composition and coverage of the library were validated, and DDRKOL was utilized to investigate modulators of TMZ response in U87MG cells. Our future work will involve characterizing different effects of DDRKOL members in radiotherapy response, in different subtypes of gliomas with different genetic BACKGROUND s. Cell response to radiation is important, therefore optimization experiments were performed with different radiation doses in A172, U373, and U373-60Gy cell lines to choose the optimal dose suitable for screening. Accordingly, 2 Gy radiation was chosen for large-scale screens. DDRKOL will serve as an important tool to study not only glioblastoma but also many other diseases that threaten global health. Discovering novel genes that affect the therapy response will be stimulating because it will help understand how to overcome therapy resistance and develop new strategies to design effective therapeutic strategies, which can ultimately translate into clinics.This study is supported by TUBITAK 1001 program (#221S439).
P09.11.A INDICATIONS AND OUTCOMES OF NERVE RECONSTRUCTIONS AFTER RESECTION OF EXTREMITY TUMORS: A SYSTEMATIC REVIEW
Authors: B Schuitema, C Y M Jansma, E Martin, J H Coert
Journal: Neuro-Oncology (2023)

Abstract AIMS Peripheral nerve injuries resulting from tumor resection are unusual, but occasionally unavoidable. It can result in serious morbidity in motor deficits, sensory deficits, and even chronic pain. Nerve reconstruction after tumor resection is possible but rarely performed and outcomes are unclear. This study creates an overview of the indications and outcomes for nerve reconstructions after tumor resections. METHODS A systematic review was performed in March 2022 in PubMed and Embase according to the PRISMA guidelines. Search terms related to “tumor” and “nerve reconstruction” were used. Studies evaluating nerve reconstructions (nerve graft, transfer or coaptation) after tumor resection in extremities were included. A qualitative synthesis was performed on all studies. Patients with accurate description of their functional abilities were assigned to minimum grade on the MRC-scale. RESULTS Fifty-nine articles were included for quality synthesis after full text screening. A total of 84 patients were described of which 40 after resection of malignant tumors. Most patients improved in motor and sensory function after nerve reconstruction. In patients with benign tumors, 79% demonstrated functional recovery on the Medical Research Council (MRC) scale of ≥3, while 77% of patients with malignant tumors showed the same level of recovery. Most patients, 85%, recovered to a protective sensation of S2 or higher. CONCLUSION Nerve reconstruction after tumor resection can help recover both sensory and motor function. It should be considered in tumor surgery with chance of resection or damage to a nerve.
P19.06.B T2/FLAIR MISMATCH, SPECIFIC RADIOGENOMIC MARKER FOR A DIFFUSE LOW GRADE ASTROCYTOMA
Authors: U M Kwikima, N Rutabasibwa, F Fezeu, K Gousias, F Minja, C Filippi
Journal: Neuro-Oncology (2023)

Abstract A 36-year-old woman presented with recurring episodes of generalized tonic clonic seizures. An MRI from an outside institution demonstrated an intra-axial brain mass suspicious for a primary brain tumor. Repeat conventional and advanced MRI imaging revealed a primary brain mass centred on the left postcentral gyrus involving cortex and subcortical white matter. The lesion was homogenously hyperintense on T2-weighted imaging, and centrally iso-to hypointense on FLAIR with a rim of hyperintense signal on the FLAIR sequence. There was no significant peritumoral edema or minimal effacement of the central sulcus. No abnormal enhancement was seen post-contrast. The lesion demonstrated no reduced diffusivity on diffusion-weighted imaging. MR perfusion showed no elevation in regional cerebral blood volume or flow. Findings are most compatible with a low grade glioma. Patient underwent total surgical resection and biopsy for histopathology. Genetic sequencing revealed an IDH mutant, non 1P,19q codeleted grade II astrocytoma. The diagnosis of adult infiltrating gliomas is predicted using imaging, and confirmed by histopathology, and molecular diagnostic methods. Regardless of grade the 1st phase in glioma diagnosis and management is IDH status. A multidisciplinary approach to the diagnosis of low grade and high grade glioma including genetic and molecular analysis is essential, as different genetic and molecular subtypes have different management and prognostic implications. Conventional MRI still represents a mandatory and extremely important step in the diagnostic workflow of neuro oncological patients for preoperative diagnosis, treatment planning, and subsequent follow up. The T2/FLAIR mismatch sign describes the MRI appearance of an IDH-mutant astrocytoma that is non 1p19q codeleted, and it is considered a preoperative novel specific MRI marker for this type of diffuse astrocytoma. In this case, the MRI findings were used preoperatively as a noninvasive tool to diagnose the patient`s low grade glioma which was confirmed by subsequent histological and genetic analysis. TEACHING POINTS1. T2/FLAIR mismatch allows for pre-operative diagnosis of IDH-mutant astrocytomas with a high level of specificity.2. It is particularly helpful in distinguishing diffuse astrocytoma from an oligodendroglioma3. Conventional MR sequences can suggest the diagnosis of IDH mutant gliomas which can assist neurosurgeons in presurgical planning and can help neuro-oncologists with treatment planning including potential clinical trials.